It's because there, technically, should only be one EFI boot partition. Microsoft just assumes that the first EFI partition it finds is the real one and it 'fixes' it automatically.
Good for the average user who just wants their computer to turn on, but bad if you're trying to dual boot.
When I was still dual booting, I'm 100% linux now, I kept my Linux bootloader on a USB so Windows couldn't break it.